Not all editors explain "I'll do" and the explanations aren't always the same.
The edition by Barbara A. Mowat and Paul Werstine (Folger Shakespeare Library, 2003, page 14) has a gloss saying that "like" (in the preceding line) means "in the form of" but has nothing for "I'll do".
The edition by Burton Raffel (The Annotated Shakespeare, Yale University Press, 2005, page 11) merely says that the line is "intoned, with a gleeful malice" but lets the reader guess the meaning.
The edition by G. K. Hunter (New Penguin Shakespeare (Penguin, 1967, page 141) has the following gloss for "do":
as in the modern vague abusive 'I'll do him' = 'I'll cause him harm'.
The edition by John Dover Wilson (The New Shakespeare, Cambridge University Press, 1947, page 100) has the following endnote for "do":
Most edd. assumes that she gnaws a hole in the hull. But this contradicts l. 24. What she will 'do' is left mysterious, until she unfolds her scheme of making 'the voyage one long torture' (K.).
("K." refers to G. L. Kittredge's edition.)
The edition by Jonathan Bate and Erik Rasmussen (The RSC Shakespeare, Macmillan, 2009, page 27) has the following gloss for "do":
act/have sex (it was thought that witches often seduced their male victims)
The edition by Nicholas Brooke (The Oxford Shakespeare, Oxford University Press, 1999, page 101) does not gloss "do" but tells us the following about "rat without a tail":
Steevens (1793) stated that old writers rationalized defective transformation by claiming that no part of a women could be changed into a tail, but he cites no authority. Thomas (p. 529) states that allusions to animal transformation are rare.
("Steevens" refers to George Steevens, who published a variorum edition of Shakespeare's plays in the 1790s. "Thomas" is a reference to Religion and the Decline of Magic (1971) by Keith Thomas, which is something of a classic on popular beliefs in sixteenth- and seventeenth-century England.)
Kenneth Muir (Arden Shakespeare, Routledge, 1984, page 12) prefers the explanation given in Witchcraft in Old and New England (1929) by G. L. Kittredge, who wrote that
she will take the shape of a rat in order to slip on board the Tiger unnoticed. This, and not to use her teeth, is the object of the transformation. There she will bewitch the craft and lay a spell upon the captain. There is no question of scuttling the ship.
A. R. Braunmuller (The New Cambridge Shakespeare, Cambridge University Press, 1997, page 110) glosses "do" as "act; fornicate" and adds the following quote from Frances Dolan's book Dangerous Familiars: Representations of Domestic Crime in England 1550–1700 (1994, page 212):
Many dramatizations of witches as powerful, dangerous agents associate their agency with female sexual desire.
Robert S. Miola's edition (Norton Critical Editions. W. W. Norton, 2014, page 7) has the following gloss for "do":
(1) act; (2) have sexual intercourse.
In short, editors don't fully agree about what the weird sister will "do". Glosses suggesting a sexual meaning are limited to relatively recent editions (Braunmuller, Miola, Bate & Rasmussen), almost as if older editions were too "Victorian" to mention that.
However, the first weird sister's (or the first witch's) next speech explains what she'll do. First, she'll make sure that the ship will endure many storms without perishing. Second, she "will drain [the sailor] dry as hay", which seems to justify the sexual explanation of "do".
The threefold repetition is part of a pattern in the play: three witches, three murderers of Banquo, "Thrice to thine and thrice to mine, ..." (in Act I, scene 3), "Had I three ears" (in Act 4, scene 1), etcetera.